biogems.info - gems for bioinformatics

New: CloudBioLinux packages are now listed on biogems.info !

#	biogem	description	by	version	released	stars	issues	total	7d	90d**)
								downloads	commits
1	bio	Bioinformatics library (...)	BioRuby project	1.4.3.0001	9 months	30	17	57317	0	10
2	biodiversity	Parser of scientific names (...)	Dmitry Mozzherin	3.1.4	11 weeks	10	5	31952	0	9
3	bio gem	Biogem is a software generator for Ruby in (...)	Raoul J.P. Bonnal, Pjotr Prins	1.3.5	7 months	14	11	26569	0	0
4	bio samtools	Binder of samtools for Ruby, on the top (...)	Ricardo Ramirez-Gonzalez, Dan MacLean, Raoul J.P. Bonnal	0.6.2	1 week	15	4	20745	0	12
5	entrez	Http requests to entrez e-utilities (...)	Jared Ning	0.5.8.1	2 years	4	...	17067	0	0
6	bio ucsc api	The Ruby ucsc api: accessing the ucsc genome (...)	Hiroyuki Mishima, Jan Aerts	0.6.0	2 months	13	1	16046	0	28
7	intermine	Webservice client library for intermine data-warehouses (...)	Alex Kalderimis	1.04.00	8 months			15612
8	bio gff3	Gff3 parser for big data (...)	Pjotr Prins	0.9.1	18 months	6	2	13605
9	sequenceserver	Blast search made easy! (...)	Anurag Priyam, Ben J Woodcroft, Yannick Wurm	0.8.7	6 weeks	30	30	13480
10	bio gadget	Gadgets for bioinformatics (...)	Shintaro Katayama	0.4.8	9 months		...	13417	0	0
11	bio maf	Maf parser for BioRuby (...)	Clayton Wheeler	1.0.1	19 months	10	29	11461
12	bio logger	Log4r wrapper with extra features for roles and (...)	Pjotr Prins	1.0.1	23 months	4	2	9906	0	0
13	bio grid	A biogem to submit jobs on a queue (...)	Francesco Strozzi	0.3.3	16 months	5	...	9599	0	0
14	bio svgenes	Create pretty svg-format images of features, gene models (...)	Dan MacLean	0.4.1	9 weeks	7	5	8465	0	11
15	bio blastxmlparser	Very fast blast xml parser and library for (...)	Pjotr Prins	1.1.1	13 months	9	...	7845
16	bio faster	A fast parser for fastq files (...)	Francesco Strozzi	0.4.5	21 months	9	...	7574	0	0
17	bio alignment	Support for multiple sequence alignments (msa) (...)	Pjotr Prins	0.0.7	20 months	6	4	7065	0	0
18	bio phyta	Pipeline to remove contaminations from est libraries (...)	Philipp Comans	0.9.4	2 years	1	1	6781	0	0
19	bio dbla classifier	A tool to classify and manipulate pfemp1 dbl-alpha (...)	George Githinji	0.7.1	12 months	1	...	6411	0	0
20	scaffolder	Build genome output files (...)	Michael Barton	0.5.0	7 months		...	6275
21	bio table	Swiss army knife of tabulated data; transforming/filtering tab/csv (...)	Pjotr Prins	0.9.0	1 week	7	18	6211	0	24
22	bio assembly	BioRuby assembly plugin (...)	Chase Miller, Francesco Strozzi	0.1.0	3 years	4	...	6017	0	0
23	bio bigbio	Low memory sequence emitters (...)	Pjotr Prins	0.1.5	10 months	8	1	5824
24	genfrag	This is a development release (...)	Pjotr Prins and Trevor Wennblom	0.0.0.4	4 years			5665
25	bio nexml	BioRuby plugin for reading and writing nexml (http://nexml.org) (...)	Rutger Vos, Anurag Priyam	1.1.0	22 months	6	1	5577
26	eutils	Lightweight Ruby api for ncbi eutils (...)	Joon Lee, aka seouri	0.2.1	8 months	6	...	5517	0	0
27	bio signalp	A wrapper for the signal peptide prediction algorith (...)	Ben J Woodcroft	0.3.0	18 months	1	...	5449	0	0
28	bio isoelectric point	A BioRuby plugin for calculating the isoelectric point (...)	George Githinji, Pascal Betz	0.1.3	2 years	3	...	5346	0	0
29	bio tm hmm	A BioRuby plugin for interaction with the transmembrane (...)	Ben J. Woodcroft	0.2.2	15 months	2	...	5343	0	0
30	bio graphics	Library for visualizing genomic regions (...)	Jan Aerts	1.4	6 years			5332
31	bio sambamba	Ruby wrapper for sambamba tool (...)	Artem Tarasov	0.0.5	18 months	2	...	5028	0	0
32	bio genomic interval	A BioRuby plugin: handling genomic interavals and overlaps (...)	Hiroyuki Mishima	0.1.2	2 years	3	...	4951	0	0
33	bio ngs	Bio-ngs provides a framework for handling ngs data (...)	Francesco Strozzi, Raoul J.P. Bonnal	0.5.2	21 months	27	14	4795
34	biointerchange	An open source framework for transforming heterogeneous data (...)	Joachim Baran, Kevin B. Cohen, Geraint Duck et al.	1.0.1	6 months	7	3	4696	0	4
35	bio octopus	Running and parsing of the protein transmembrane domain (...)	Ben J Woodcroft	0.1.1	2 years	1	...	4664	0	0
36	bio kmer counter	A biogem for counting small kmers for fingerprinting (...)	Ben J Woodcroft	0.1.2	9 months	5	...	4622	0	0
37	goruby	Gene ontology (go) interface for Ruby (...)	Ben J Woodcroft	0.2.0	3 years	8	...	4157	0	0
38	bio band	Data mining algorithms for jRuby (...)	arrigonialberto86	0.1.11	5 months	13	3	4093	0	0
39	bio bwa	Ruby binding for bwa mapping software (...)	Francesco Strozzi	0.2.2	2 years	3	...	3918
40	ruby ensembl api	Api to ensembl databases (...)	Jan Aerts, Francesco Strozzi	1.0.1	3 years	30	4	3904	0	0
41	bio lazyblastxml	A plugin that allows you to parse large (...)	robsyme	0.4.0	2 years	1	...	3754
42	bio bgzf	Reading/writing bgzf blocks (...)	Artem Tarasov, Clayton Wheeler	0.2.1	19 months	2	...	3683	0	0
43	bio publisci	Publish scientific results to the semantic web (...)	Will Strinz	0.1.0	5 months		...	3648
44	bio pileup iterator	Iterate through a samtools pileup file (...)	Ben J. Woodcroft	0.0.4	15 months	1	...	3555	0	0
45	bio kb illumina	Geneexpression illuminahumanannotation (...)	Raoul J.P. Bonnal	0.1.0	3 years	1	...	3104	0	0
46	bio cd hit report	Read and manipulate cd-hit clusters (...)	George Githinji	0.1.0	10 months	2	1	3076
47	bio plasmoap	Implementation of the plasmoap algorithm (...)	Ben J Woodcroft	0.0.2	2 years	1	...	3071	0	0
48	bio rdf	Bioinformatics triple-store support (...)	Pjotr Prins	0.0.2	21 months	4	1	2775	3	75
49	bio gff3 pltools	Ruby wrapper for the gff3-pltools (...)	Marjan Povolni	0.3.0	19 months			2749
50	bio tabix	Ruby binding for samtools tabix (...)	throwern	1.0.1	5 months	3	...	2737	0	0
51	bio affy	Parse affymetrix cel/cdf files (...)	Pjotr Prins	0.5.1	2 years	2	1	2707	0	0
52	bio chembl	Chembl rest api client, parser and container (...)	Mitsuteru Nakao	0.1.3	19 months	1	1	2680	0	0
53	bio ucsc util	Ruby binding to the ucsc kent utilities (...)	throwern	0.1.2	17 months	1	...	2649	0	0
54	bio gngm	Next-generation mapping of mutations (...)	Dan MacLean	0.2.1	15 months	1	...	2647
55	bio core	BioRuby core plugins, most and stable plugins. blastxmlparser, (...)	Raoul J.P. Bonnal	0.0.1	2 years	1	...	2563	0	0
56	bio cnls screenscraper	Programmatic interface to the cnls nuclear localisation signal (...)	Ben J. Woodcroft	0.3.0	22 months	1	...	2384	0	0
57	bio wolf psort wrapper	Enables the localisation predictor wolf psort to be (...)	Ben J Woodcroft	0.0.3	2 years	1	...	2340	0	0
58	bio basespace sdk	Basespace Ruby sdk is a Ruby based software (...)	Joachim Baran, Raoul Bonnal, Eri Kibukawa et al.	0.1.7	7 months	8	2	2126	0	0
59	bio hmmer model	Parse pfam hmm definition files (...)	Ben J. Woodcroft	0.0.2	21 months	1	...	1995	0	0
60	bio protparam	A protparam compatible utility for BioRuby (...)	hryk	0.2.0	14 months	1	...	1937	0	6
61	bio unichem	BioRuby plugin for unichem rest web service (...)	Mitsuteru Nakao	0.3.0	13 months		...	1896
62	bio gag	Bio-gag is a biogem for detecting and correcting (...)	Ben J Woodcroft	0.1.0	16 months	2	...	1836
63	bio synreport	Reports whether a nucleotide change results in synonymous (...)	Dan MacLean	0.1.2	9 months		...	1773	0	0
64	bio krona	This biogem is built around krona, a flashy (...)	Ben J. Woodcroft	0.1.1	6 months	1	...	1745	0	0
65	bio sge	BioRuby plugin for sun grid engine (...)	Toshiaki Katayama	0.0.0	3 years	4	...	1613	0	0
66	bio restriction enzyme	Digests dna based on restriction enzyme cut patterns (...)	Trevor Wennblom	1.0.0	2 years		1	1598	0	0
67	bio hello	Hello world plugin for the BioRuby (just for (...)	Toshiaki Katayama	0.0.0	3 years	3	...	1594	0	0
68	dna sequence aligner	Does high pairwise alignment of sequencing reads with (...)	John T. Prince	0.0.2	4 years			1580
69	bio statsample timeseries	Timeseries modules for statsample (...)	Ankur Goel, Claudio Bustos	0.2.1	5 months		...	1527
70	bio emboss six frame nucleotide sequences	A method to get the nucleotide sequence of (...)	Ben J Woodcroft	0.1.0	2 years	1	...	1354	0	0
71	bio core ext	BioRuby core ext: plugins which require external library (...)	Raoul J.P. Bonnal, Pjotr Prins	0.0.1	2 years	1	...	1340	0	0
72	bio data restriction enzyme	Restriction enzyme dataset (...)	Sir Richard J. Roberts, Trevor Wennblom	1.109.0	2 years		...	1300	0	0
73	bio biolinux	Meta package for biolinux distribution (...)	Raoul J.P. Bonnal	0.1.0	2 years	2	...	1292	0	0
74	bio ensembl	A Ruby api to the ensembl database (...)	Jan Aerts, Francesco Strozzi	1.1.0	2 years	3	...	1279
75	bio foo	One-line summary of your gem (...)	Toshiaki Katayama	0.0.0	2 years	1	...	1276
76	bio dbsnp	Decoding the dbsnp bitfield (...)	Hiroyuki Mishima	0.1.1	2 years	2	...	1246	0	0
77	bio phyloxml	Phyloxml plugin for BioRuby (...)	Diana Jaunzeikare, Clayton Wheeler	0.9.0	21 months	3	...	1237	0	0
78	bio exportpred	Wrapper around the exportpred algorithm for predicting p (...)	Ben J Woodcroft	0.0.1	2 years	1	...	1219
79	bio aliphatic index	A simple biogem that allows computation of the (...)	Ben J Woodcroft	0.0.1	2 years	1	...	1199
80	bio hydropathy	Hydropathy scale for BioRuby (...)	Ben J Woodcroft	0.0.1	2 years	1	...	1186	0	0
81	intermine bio	Biological extensions for the intermine webservice client library (...)	Alex Kalderimis	0.98.1	2 years			1100
82	bio hmmer3 report	Enables parsing of hmmer version 3 reports (...)	Christian Zmasek, Ben J Woodcroft	0.0.1	22 months	1	1	1065
83	bio incanter	Build graph with jRuby (...)	Matteo Picciolini	0.1.0	19 months		...	987
84	bio ipcress	A programmatic interface to the ipcress in-silico pcr (...)	Ben J Woodcroft	0.0.1	19 months	1	...	960	0	0
85	bio gggenome	Gggenome Ruby client (...)	Mitsuteru Nakao	0.2.0	6 months	1	...	845	0	0
86	bio ensembl rest	Ruby ensembl rest api (...)	Alberto Donizetti	0.2.0	5 months	2	...	763	0	0
87	bio img metadata	Reads metadata from integrated microbial genomes (img) metadata (...)	Ben J. Woodcroft	0.0.1	14 months		...	739
88	bio statsample glm	Generalized linear models for statsample (...)	Ankur Goel	0.1.1	5 months		...	729
89	bio stockholm	Parse stockholm sequence alignment format (...)	Ben J. Woodcroft	0.0.1	8 months	2	...	511	0	0
90	bio raxml	Ruby wrapper to run standard-raxml for maximum likelihood (...)	Fernando Izquierdo	0.1.0	7 months		...	456
91	bio velvet	Parser to work with file formats used in (...)	Ben J Woodcroft	0.1.0	9 weeks		...	448	0	17
92	bio commandeer	Dead simple method of running shell commands from (...)	Ben J. Woodcroft	0.1.0	8 weeks		...	402	0	13
93	bio express beta diversity	Interface for express beta diversity (...)	Ben J. Woodcroft	0.1.0	6 weeks		...	380	0	8
94	bio repeatmasker	Bio-repeatmasker (...)	Andrei Rozanski	0.0.3	8 weeks			367
95	bio qtlHD	(...) pre		pre				314
96	bio vcf	Vcf parser (...)	Pjotr Prins	0.0.2	5 days		...	244	18	51
97	bio cigar	A parser for cigar format alignments (...) new	Ben J Woodcroft	0.1.0	1 week	1	...	190	0	6
98	bio exominer	Mine publications for gene names (...) new	Pjotr Prins	0.0.3	1 week		...	85	0	19

*) gem downloads (total & last 90 days) from rubygems.org as of 2014-03-10
**) number of commits on GitHub (last 7 days & last 90 days)